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NAMESPACE
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NAMESPACE
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# Generated by roxygen2: do not edit by hand
S3method(SNF,liger)
S3method(SNF,list)
S3method(optimizeALS,liger)
S3method(optimizeALS,list)
S3method(quantileAlignSNF,liger)
S3method(quantileAlignSNF,list)
export(Matrix.column_norm)
export(SNF)
export(aggregateByCluster)
export(calcARI)
export(calcAgreement)
export(calcAlignment)
export(calcAlignmentPerCluster)
export(calcDatasetSpecificity)
export(calcPurity)
export(clusterLouvainJaccard)
export(convertOldLiger)
export(createLiger)
export(getFactorMarkers)
export(getGeneValues)
export(getProportionMito)
export(imputeKNN)
export(ligerToSeurat)
export(makeRiverplot)
export(normalize)
export(optimizeALS)
export(optimizeNewData)
export(optimizeNewK)
export(optimizeNewLambda)
export(optimizeSubset)
export(plotByDatasetAndCluster)
export(plotClusterFactors)
export(plotClusterProportions)
export(plotFactors)
export(plotFeature)
export(plotGene)
export(plotGeneLoadings)
export(plotGeneViolin)
export(plotGenes)
export(plotWordClouds)
export(quantileAlignSNF)
export(quantile_norm)
export(read10X)
export(removeMissingObs)
export(reorganizeLiger)
export(runTSNE)
export(runUMAP)
export(scaleNotCenter)
export(scaleNotCenter_sparse)
export(selectGenes)
export(seuratToLiger)
export(subsetLiger)
export(suggestK)
export(suggestLambda)
exportClasses(liger)
import(Matrix)
import(doSNOW)
importFrom(FNN,get.knn)
importFrom(FNN,get.knnx)
importFrom(Matrix,colSums)
importFrom(Matrix,rowMeans)
importFrom(Matrix,rowSums)
importFrom(Matrix,sparseMatrix)
importFrom(Matrix,t)
importFrom(RANN.L1,nn2)
importFrom(Rcpp,evalCpp)
importFrom(Rtsne,Rtsne)
importFrom(cowplot,plot_grid)
importFrom(dplyr,"%>%")
importFrom(dplyr,group_by)
importFrom(dplyr,group_cols)
importFrom(dplyr,mutate_at)
importFrom(dplyr,summarize)
importFrom(dplyr,vars)
importFrom(foreach,"%dopar%")
importFrom(foreach,foreach)
importFrom(ggplot2,aes)
importFrom(ggplot2,aes_string)
importFrom(ggplot2,annotate)
importFrom(ggplot2,coord_cartesian)
importFrom(ggplot2,coord_fixed)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,geom_boxplot)
importFrom(ggplot2,geom_line)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_text)
importFrom(ggplot2,geom_violin)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggtitle)
importFrom(ggplot2,guide_legend)
importFrom(ggplot2,guides)
importFrom(ggplot2,labs)
importFrom(ggplot2,scale_color_gradient)
importFrom(ggplot2,scale_color_gradient2)
importFrom(ggplot2,scale_color_gradientn)
importFrom(ggplot2,scale_color_viridis_c)
importFrom(ggplot2,scale_size)
importFrom(ggplot2,scale_x_continuous)
importFrom(ggplot2,scale_y_continuous)
importFrom(ggplot2,scale_y_discrete)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_bw)
importFrom(ggplot2,theme_classic)
importFrom(ggplot2,xlab)
importFrom(ggplot2,ylab)
importFrom(ggrepel,geom_text_repel)
importFrom(grid,gpar)
importFrom(grid,roundrectGrob)
importFrom(grid,unit)
importFrom(ica,icafast)
importFrom(irlba,prcomp_irlba)
importFrom(mclust,adjustedRandIndex)
importFrom(methods,"slot<-")
importFrom(plyr,mapvalues)
importFrom(plyr,rbind.fill.matrix)
importFrom(riverplot,makeRiver)
importFrom(riverplot,riverplot)
importFrom(snow,makeCluster)
importFrom(snow,stopCluster)
importFrom(stats,optimize)
importFrom(stats,quantile)
useDynLib(liger)